Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold668
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 52720
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:5076 original size:11 final size:12
Alignment explanation
Indices: 5046--5092 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
5036 CCGTATGCAA
*
5046 ATTTTTTTTTCAAA
1 ATTTTTTTTTC--G
*
5060 ATTTTTTTTTTG
1 ATTTTTTTTTCG
5072 ATTTTTTTTTCG
1 ATTTTTTTTTCG
5084 ATTTTTTTT
1 ATTTTTTTT
5093 GAATCTACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
12 20 0.67
14 10 0.33
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.77
Consensus pattern (12 bp):
ATTTTTTTTTCG
Found at i:7073 original size:14 final size:14
Alignment explanation
Indices: 7056--7095 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
7046 CGAATGGAAT
*
7056 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
7070 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
7084 GATATGAACAAA
1 GGTAGGAACAAA
7096 TTGGTCAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:9459 original size:23 final size:22
Alignment explanation
Indices: 9407--9459 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
9397 TCCACGTCTT
*
9407 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
9429 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
9452 TTTCTTTT
1 TTTCTTTT
9460 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:11729 original size:6 final size:6
Alignment explanation
Indices: 11718--11742 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
11708 TAATTAGAAC
11718 ACTAAA ACTAAA ACTAAA ACTAAA A
1 ACTAAA ACTAAA ACTAAA ACTAAA A
11743 AAACTCCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (6 bp):
ACTAAA
Found at i:19129 original size:93 final size:93
Alignment explanation
Indices: 18970--19139 Score: 250
Period size: 93 Copynumber: 1.8 Consensus size: 93
18960 TAGGAGTTGA
* * *
18970 GCATCCAAACTCGTTGAGTTGAGTCCGACTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGACATCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
*
19035 TGAGTCCGAGTTTGTGAGATGTAACTAG
66 TGAGTCCAAGTTTGTGAGATGTAACTAG
* * * * *
19063 GCATCCGAACTCGTTGAGTTGAGTCCGAGATCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGACATCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
*
19128 TGGGTCCAAGTT
66 TGAGTCCAAGTT
19140 CACTTAGGGG
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
93 67 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGACATCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCAAGTTTGTGAGATGTAACTAG
Found at i:19407 original size:19 final size:20
Alignment explanation
Indices: 19370--19407 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
19360 ATAAGGTGGT
19370 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
19390 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
19408 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:22348 original size:30 final size:30
Alignment explanation
Indices: 22314--22410 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
22304 TAAACTAAAA
22314 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * * *
22344 TGAGCGGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGC-TAAGCTTTAGCTCGTGAGCTAAAGT
* *
22374 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
22404 TGAGCTA
1 TGAGCTA
22411 GGAATGAGCT
Statistics
Matches: 48, Mismatches: 16, Indels: 6
0.69 0.23 0.09
Matches are distributed among these distances:
29 2 0.04
30 40 0.83
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.27
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:23790 original size:20 final size:20
Alignment explanation
Indices: 23767--23814 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
23757 AGCTCCGTCC
23767 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTCAGCTCATTTG
*** * *
23787 AGCTCGTTTTAGCTCGTTTG
1 AGCTCAACTCAGCTCATTTG
23807 AGCTCAAC
1 AGCTCAAC
23815 CGAGCTTACT
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTG
Found at i:27066 original size:26 final size:26
Alignment explanation
Indices: 27037--27145 Score: 157
Period size: 26 Copynumber: 4.2 Consensus size: 26
27027 ATGCTACAAA
27037 ATGATAATGTG-TTAGGTAAATGTTCC
1 ATGATAATG-GATTAGGTAAATGTTCC
*
27063 ATGATAATGGATTAGGTAAATATTCC
1 ATGATAATGGATTAGGTAAATGTTCC
* *
27089 ATGACAATGGGTTAGGTAAATGTTCC
1 ATGATAATGGATTAGGTAAATGTTCC
* *
27115 ATGATAATGGTTTAGGAAAATGTTCC
1 ATGATAATGGATTAGGTAAATGTTCC
27141 ATGAT
1 ATGAT
27146 GGGCATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
25 1 0.01
26 74 0.99
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.35
Consensus pattern (26 bp):
ATGATAATGGATTAGGTAAATGTTCC
Found at i:32008 original size:13 final size:13
Alignment explanation
Indices: 31956--32025 Score: 58
Period size: 12 Copynumber: 5.5 Consensus size: 13
31946 TTTTGCTCGA
*
31956 TTTTTTTC-ACTT
1 TTTTTTTCGAATT
*
31968 TTTTTTT-GATTT
1 TTTTTTTCGAATT
*
31980 TTTTTTTCAATCAATT
1 TTTTTTTC---GAATT
31996 TTTTTTTCGAATT
1 TTTTTTTCGAATT
32009 TTTTTTT-G-ATT
1 TTTTTTTCGAATT
32020 TTTTTT
1 TTTTTT
32026 GTTACTCCAA
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
11 9 0.18
12 18 0.37
13 11 0.22
16 11 0.22
ACGTcount: A:0.13, C:0.07, G:0.04, T:0.76
Consensus pattern (13 bp):
TTTTTTTCGAATT
Found at i:36488 original size:29 final size:30
Alignment explanation
Indices: 36438--36495 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
36428 TGAGTGATAA
*
36438 AAAAAGAGAGAGTGATTCAAAA-GAAAAAG
1 AAAAAGAAAGAGTGATTCAAAATGAAAAAG
*
36467 AAAAAGAAACGAGTGA-TGAAAATGAAAAA
1 AAAAAGAAA-GAGTGATTCAAAATGAAAAA
36496 AAGAGTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.64, C:0.03, G:0.22, T:0.10
Consensus pattern (30 bp):
AAAAAGAAAGAGTGATTCAAAATGAAAAAG
Found at i:38245 original size:20 final size:20
Alignment explanation
Indices: 38199--38245 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
38189 AGCTCGTTTC
*
38199 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
38219 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
38239 CAGCTCA
1 CAGCTCA
38246 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:38988 original size:22 final size:22
Alignment explanation
Indices: 38958--39001 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
38948 TTTGGTATTT
38958 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
38980 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
39002 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:41435 original size:14 final size:14
Alignment explanation
Indices: 41416--41449 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
41406 AGGAAATTTG
41416 AAAAAAAAATTCAA
1 AAAAAAAAATTCAA
41430 AAAAAAAAATTCAA
1 AAAAAAAAATTCAA
41444 AAAAAA
1 AAAAAA
41450 TCGAAGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (14 bp):
AAAAAAAAATTCAA
Found at i:42557 original size:48 final size:47
Alignment explanation
Indices: 42478--42583 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
42468 GAGTGTCATG
*
42478 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
42526 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
42574 GAAAAAGAAA
1 GAAAAAGAAA
42584 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:44152 original size:20 final size:20
Alignment explanation
Indices: 44129--44182 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
44119 AGTTTTTCCC
*
44129 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
44149 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
44169 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
44183 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:44164 original size:30 final size:30
Alignment explanation
Indices: 44129--44202 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
44119 AGTTTTTCCC
44129 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
44159 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
44189 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
44203 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:44192 original size:20 final size:20
Alignment explanation
Indices: 44129--44193 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
44119 AGTTTTTCCC
* * * *
44129 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
44149 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
44168 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
44189 AGCTC
1 AGCTC
44194 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:45802 original size:12 final size:12
Alignment explanation
Indices: 45787--45843 Score: 55
Period size: 11 Copynumber: 4.7 Consensus size: 12
45777 AAAACCAATC
45787 AAAAAAATTCGA
1 AAAAAAATTCGA
*
45799 AAAAAAATTGATTGA
1 AAAAAAA-T--TCGA
45814 AAAAAAATTC-A
1 AAAAAAATTCGA
*
45825 AAAAAAAGT-GA
1 AAAAAAATTCGA
45836 AAAAAAAT
1 AAAAAAAT
45844 CGAGCAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
11 17 0.46
12 8 0.22
13 1 0.03
14 1 0.03
15 10 0.27
ACGTcount: A:0.70, C:0.04, G:0.09, T:0.18
Consensus pattern (12 bp):
AAAAAAATTCGA
Found at i:47012 original size:18 final size:17
Alignment explanation
Indices: 46925--47015 Score: 62
Period size: 17 Copynumber: 5.2 Consensus size: 17
46915 GAAAGAAACA
46925 AAAAGAAAA--AAAAAG
1 AAAAGAAAATGAAAAAG
* *
46940 AAAAGAAATTGCAAAAG
1 AAAAGAAAATGAAAAAG
*
46957 AAAA-AGAAATCAAAAAG
1 AAAAGA-AAATGAAAAAG
* * *
46974 TGAGAGAAAAAGAAATGAAG
1 -AAAAGAAAATGAAA--AAG
46994 AAAAGAAAATTGAAAAAG
1 AAAAGAAAA-TGAAAAAG
47012 AAAA
1 AAAA
47016 AGCGAAAAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 13
0.69 0.15 0.16
Matches are distributed among these distances:
15 8 0.14
16 1 0.02
17 17 0.30
18 15 0.27
19 8 0.14
20 7 0.12
ACGTcount: A:0.73, C:0.02, G:0.18, T:0.08
Consensus pattern (17 bp):
AAAAGAAAATGAAAAAG
Found at i:47035 original size:13 final size:13
Alignment explanation
Indices: 46980--47035 Score: 51
Period size: 14 Copynumber: 4.2 Consensus size: 13
46970 AAAGTGAGAG
46980 AAAAAGAAA-TGA
1 AAAAAGAAATTGA
46992 AGAAAAGAAAATTGA
1 A-AAAAG-AAATTGA
* **
47007 AAAAGAAAAAGCGA
1 AAAA-AGAAATTGA
47021 AAAAAGAAATTGA
1 AAAAAGAAATTGA
47034 AA
1 AA
47036 GAGAGCTTGA
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
12 1 0.03
13 13 0.38
14 15 0.44
15 5 0.15
ACGTcount: A:0.71, C:0.02, G:0.18, T:0.09
Consensus pattern (13 bp):
AAAAAGAAATTGA
Found at i:48884 original size:20 final size:20
Alignment explanation
Indices: 48861--48914 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
48851 AGTTTTTCCC
*
48861 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
48881 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
48901 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
48915 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:48896 original size:30 final size:30
Alignment explanation
Indices: 48861--48934 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
48851 AGTTTTTCCC
48861 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
48891 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
48921 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
48935 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:48924 original size:20 final size:20
Alignment explanation
Indices: 48861--48925 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
48851 AGTTTTTCCC
* * * *
48861 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
48881 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
48900 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
48921 AGCTC
1 AGCTC
48926 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:50652 original size:20 final size:21
Alignment explanation
Indices: 50605--50652 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
50595 TTAGCTTTTC
*
50605 CAGCTCACGTCGAGCTCAAGT
1 CAGCTCACGTCAAGCTCAAGT
* *
50626 CAACTCAC-TCAAGCTCAATT
1 CAGCTCACGTCAAGCTCAAGT
50646 CAGCTCA
1 CAGCTCA
50653 ATCTAACCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.29, C:0.35, G:0.15, T:0.21
Consensus pattern (21 bp):
CAGCTCACGTCAAGCTCAAGT
Done.